Century-old chromatin architecture revealed in formalin-fixed vertebrates

• Published in: Nature communications Vol. 15; no. 1; pp. 6378 - 14
• Main Authors: Hahn, Erin E., Stiller, Jiri, Alexander, Marina R., Grealy, Alicia, Taylor, Jennifer M., Jackson, Nicola, Frere, Celine H., Holleley, Clare E.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.07.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/15; 38/23; 38/91; 45; 45/22; 45/23; 631/1647/2210/2211; 631/181/2474; 631/208/212/177; 631/337/100/101; 64; 64/60; Animal models; Animals; Biodiversity; Biological collections; Chromatin; Chromatin - genetics; Chromatin - metabolism; Differentiation (biology); Environmental conditions; Environmental effects; Environmental impact; Environmental stress; Female; Fixatives - chemistry; Formaldehyde; Gene expression; Humanities and Social Sciences; Male; multidisciplinary; Museum collections; Museums; Phenotypes; Phenotypic variations; Preservatives; Science; Science (multidisciplinary); Tissue Fixation - methods; Vertebrates; Vertebrates - genetics; Yeast; Yeasts
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50668-4

Gene expression is regulated by changes in chromatin architecture intrinsic to cellular differentiation and as an active response to environmental stimuli. Chromatin dynamics are a major driver of phenotypic diversity, regulation of development, and manifestation of disease. Remarkably, we know little about the evolutionary dynamics of chromatin reorganisation through time, data essential to characterise the impact of environmental stress during the ongoing biodiversity extinction crisis (20 th –21 st century). Linking the disparate fields of chromatin biology and museum science through their common use of the preservative formaldehyde (a constituent of formalin), we have generated historical chromatin profiles in museum specimens up to 117 years old. Historical chromatin profiles are reproducible, tissue-specific, sex-specific, and environmental condition-dependent in vertebrate specimens. Additionally, we show that over-fixation modulates differential chromatin accessibility to enable semi-quantitative estimates of relative gene expression in vertebrates and a yeast model. Our approach transforms formalin-fixed biological collections into an accurate, comprehensive, and global record of environmental impact on gene expression and phenotype. Formaldehyde-preserved museum specimens have produced genetic data. Here, the authors generate chromatin profiles from museum specimens 117 years old and experimentally demonstrate chromatin profile presence in formalin-fixed mouse and yeast models.